The 24-year-old midfielder, whose contract expires at the end of next season, has been heavily linked with a move to Manchester United in the summer.
But Kroos, who will be a crucial member of the defending champions' midfield against United in their Champions League quarter-final tie in the absence of the injured Thiago Alcantara, is set to stay at the Allianz Arena.
"Toni Kroos is sure to play in a Bayern Munich shirt next year as well," Rummenigge told reporters before flying to Manchester on Monday morning.
Guardiola echoed those words, albeit without offering any assurances that the Germany international would stay beyond next season.
"Toni has one year more of a contract and Toni will remain," Guardiola said.
"I hope he can extend his contract and stay with us because he is a very good guy, he loves his game, it is not just a job for him and I would like him to stay.
"I spoke with the player, with the club, I gave my opinion. After that I am not manager, I am just the trainer."